Contacts of the strand formed by residues 454 - 462 (chain A) in PDB entry 4EWS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 454 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 3.9 28.9 - - + -
264A TRP* 3.4 37.2 - + + +
265A PHE 3.2 16.2 - - - +
266A SER* 4.3 0.4 - - - -
333A CYS* 3.4 13.9 - - - +
450A THR* 3.9 0.2 - - - -
451A ARG* 2.8 59.3 + - + +
452A ASP 3.6 17.7 - - - -
453A GLY* 1.3 80.8 - - - +
455A LEU* 1.3 61.2 + - - +
456A LEU* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TRP* 3.9 0.3 - - - -
265A PHE* 3.0 38.8 + - + +
270A PHE* 3.8 33.0 - - + -
333A CYS* 4.1 2.6 - - - -
338A VAL* 4.0 13.0 - - + -
448A ILE* 3.8 17.9 - - + -
449A ILE 3.3 7.6 - - - +
450A THR* 3.7 23.6 - - + +
454A PHE* 1.3 77.0 - - - +
456A LEU* 1.3 65.7 + - - +
457A LEU* 3.7 28.9 - - + -
502A 2OB 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU 3.9 17.9 - - - +
255A LEU* 3.5 30.7 - - + -
262A TYR* 4.9 0.7 - - + -
263A PHE 3.3 20.2 - - - +
264A TRP* 4.3 6.1 - - + -
447A GLU 3.2 4.7 - - - +
448A ILE* 3.5 2.1 - - - -
449A ILE* 2.7 56.3 + - + +
451A ARG* 5.2 2.0 - - + -
454A PHE* 3.6 25.6 - - + -
455A LEU* 1.3 78.0 - - - +
457A LEU* 1.3 62.5 + - - +
458A GLN* 4.1 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU 3.7 1.2 - - - +
262A TYR* 3.4 3.5 - - - -
263A PHE* 2.7 47.5 + - + +
265A PHE* 3.8 27.6 - - + -
447A GLU 3.5 3.1 - - - +
448A ILE* 3.6 30.3 - - + -
455A LEU* 3.7 20.9 - - + -
456A LEU* 1.3 73.2 - - - +
458A GLN* 1.3 61.7 + - - +
459A MET* 3.8 17.5 - - + -
501A 2OB 4.2 13.2 - - + -
502A 2OB 3.7 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU 5.2 3.0 + - - -
256A GLY* 4.9 3.6 - - - +
259A ARG* 3.6 26.5 + - + +
261A LEU 3.4 4.9 - - - -
262A TYR* 3.4 33.2 - - + -
446A PRO* 3.4 1.6 - - - +
447A GLU* 3.0 41.5 + - + +
449A ILE* 3.8 26.0 - - + +
456A LEU* 4.4 20.7 - - + +
457A LEU* 1.3 77.2 - - - +
459A MET* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 3.5 13.8 - - - +
260A MET* 3.1 6.2 + - - -
261A LEU* 2.9 61.5 + - + +
263A PHE* 3.7 28.3 - - + -
443A ILE* 4.1 20.2 - - + -
444A ILE 4.2 0.2 - - - +
446A PRO* 4.1 15.0 - - + -
457A LEU* 3.8 23.6 - - + -
458A GLN* 1.3 76.1 - - - +
460A ASP* 1.3 69.6 + - - +
461A PHE* 5.2 1.3 - - + -
501A 2OB 4.3 15.7 - - + -
502A 2OB 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER 4.7 0.9 - - - +
259A ARG* 3.1 30.7 + - - +
260A MET* 3.0 44.1 + - + +
443A ILE* 3.7 2.6 - - - -
444A ILE* 2.8 50.2 + - + +
445A ASN* 5.6 0.7 - - - +
459A MET* 1.3 75.7 - - - +
461A PHE* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.7 14.4 - - + -
22A VAL* 4.0 13.8 - - + +
23A LEU* 3.4 32.8 - - + -
260A MET* 3.4 42.0 - - + +
261A LEU* 3.7 33.7 - - + -
441A PHE* 5.7 1.3 - - + -
442A ASP 3.3 11.0 - - - +
443A ILE* 4.9 5.2 - - + -
444A ILE* 3.6 6.9 - - - +
459A MET* 5.2 3.8 - - + -
460A ASP* 1.3 78.2 - - - +
462A GLY* 1.3 63.0 + - - +
463A PHE* 3.9 10.8 + - + -
501A 2OB 3.3 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PHE* 4.5 1.6 - - - +
442A ASP* 2.8 41.0 + - - +
444A ILE* 3.5 11.4 - - - +
461A PHE* 1.3 74.5 - - - +
463A PHE* 1.4 64.8 + - - -
464A PRO* 3.5 5.7 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il